Marin Greenwood ICF International 1

Chapter 6: Effects Analysis for Delta Smelt Appendix 5.A: CalSim II Modeling and Results Appendix 5.B: DSM2 Modeling and Results Appendix 5.G: Projects to Be Included in Cumulative Effects Analysis for the Conveyance Section 7 Biological Assessment Appendix 6.A: Quantitative Methods for Biological Assessment of Delta Smelt (Chapter 3: Description of the Proposed Action) 2

6.1 Effects on Delta Smelt Effects by life stage (request from USFWS): individual-level and population-level Effects on critical habitat: PCEs 1 (physical habitat – spawning substrate), 2 (water quality), 3 (river flow for migration/transport), 4 (salinity – low salinity zone nursery habitat) Effects of Water Facility Construction on Delta Smelt Effects of Water Facility Maintenance on Delta Smelt Effects of Water Facility Operations on Delta Smelt Effects of Conservation Measures on Delta Smelt Effects of Monitoring Activities Cumulative Effects on Delta Smelt 3

6.1.1 Effects of Water Facility Construction Generally qualitative discussion Pile-driving analysis (NMFS spreadsheet tool) assumes worst case (impact driving, no attenuation) [ ; ; ] GIS analysis for facility direct impacts (all permanent – see also Table in Chapter 3) North Delta Diversions: 13.1 acres (65.5 acres compensation) [ ] Barge landings: 22.4 acres (67.2 acres compensation) [ ] Head of Old River Operable Gate: 2.9 acres (7.5 acres compensation) [ ] 4

6.1.2 Effects of Water Facility Maintenance Qualitative discussion North Delta Intakes Barge landings Head of Old River Gate Clifton Court Forebay Critical habitat: PCEs 1 (Physical habitat – spawning substrate) and 2 (Water quality) Potential effects limited by Avoidance and Minimization Measures (AMMs) 5

6.1.3 Effects of Water Facility Operations North Delta Exports South Delta Exports Head of Old River Gate Operations Habitat Effects Delta Cross Channel Suisun Marsh Facilities North Bay Aqueduct Other Facilities Effects on Critical Habitat 6

North Delta Exports Small proportion of Delta Smelt (larvae): ~0.25% 7

North Delta Exports Examination of potential for adult Delta Smelt to tidally surf upstream to NDD (Methods: 5.B.3.6) Particles released based on migration trigger (4-river index > 20,000 cfs), day of peak Freeport flow (or Feb 1) Upper 10% of water column of flood tide, lower 10% of water column on ebb tide Result: No potential to tidally surf upstream to NDD (need to actively swim) 8

North Delta Exports Entrainment Screen size in relation to fish body size (6.A.2.2) Delta Smelt < mm could be entrained 9

North Delta Exports Impingement and Screen Contact Application of UC Davis fish treadmill equations Proposed 0.2 ft/s approach velocity Mortality increases with increasing sweeping velocity May also be difficulty passing the intakes… 10

North Delta Exports Impingement and Screen Contact Potential to migrate upstream past the fish screens at the edge of the channel (6.A ) Successful migration past the downstream-most screen unlikely (probability ~0.07) Uncertainty: use of other bank, channel bottom, screen refugia Compensation for potential reduced access to 55 acres of spawning habitat upstream of intakes [PCEs 1-3: ] 11

North Delta Exports Predation at the NDD Qualitative discussion Overall: potential for effects, but outside of species’ main range [larvae: ; migrating adults: ] 12

South Delta Exports Entrainment USFWS (2008) BiOp proportional entrainment loss regressions Migrating adults (6.A.3.1.1): Old/Middle River flows only – potentially less entrainment under PA Doesn’t capture real-time operational adjustments 13

South Delta Exports Entrainment USFWS (2008) BiOp proportional entrainment loss regressions Larvae/young juveniles (6.A.3.1.2): OMR and X2 (Mar- Jun and Apr-May) Generally similar between PA and NAA Doesn’t capture real-time operational adjustments 14

South Delta Exports Entrainment DSM2-PTM (particle tracking modeling) (6.A.3.2) Larvae Starting distribution from 20-mm survey data, matched to closest Delta outflow ( ) 15

South Delta Exports Entrainment DSM2-PTM (particle tracking modeling) Larvae Less total entrainment under PA in Mar/Jun, potentially slightly more in Apr/May in some WY types (sometimes less OMR flow because of Head of Old River gate under PA, differing San Luis Reservoir rule curve between NAA and PA; still meeting protective criteria described in Chapter 3: Table 3.3-2) Real-time operations to minimize any effects 16

South Delta Exports Entrainment DSM2-PTM (particle tracking modeling) Larvae/young juveniles 17

South Delta Exports Entrainment DSM2-PTM (particle tracking modeling) Larvae/young juveniles 18

South Delta Exports Entrainment DSM2-PTM (particle tracking modeling) Larvae/young juveniles 19

South Delta Exports Entrainment DSM2-PTM (particle tracking modeling) Larvae/young juveniles 20

South Delta Exports Predation Qualitative discussion 21

Habitat Effects Abiotic Habitat Abiotic habitat index (Feyrer et al. 2011) (6.A.4.1) Similar between NAA and PA (both have USFWS BiOp Fall X2 requirement) less > 22

Habitat Effects Water Temperature DSM2-QUAL (Attachment 3 of Appendix 5.B) Little difference (air temperature is the main driver; Wagner et al. 2011) Sediment Removal (Water Clarity) Applied methods from BDCP (essentially sediment concentration at Freeport * water diversions) Result: ~11% of Sacramento River sediment removed Possible effect on water clarity in the longer term AMM: Development/implementation of sediment reintroduction plan [ in Chapter 3] 23

Habitat Effects Entrainment of Food Web Materials (6.A.4.2) Phytoplankton carbon (Chl a * 35) removal by NDD (Density of phyto. C in inflowing Sac. R water * NDD water exported)/(Density of phyto. C at Antioch * Delta volume) 24

Habitat Effects Entrainment of Food Web Materials Result: Generally 5% or less removal by NDD Potential for offsetting by in situ production, less south Delta exports (SJR water has greater phyto. C density) 25

Habitat Effects Microcystis Flow 26

Habitat Effects Microcystis Residence time (DSM2-PTM) (6.A.4.3) Selected 25 representative years across range of flows 4,000 particles released per subregion on first of month (Jul-Nov) 27

Habitat Effects Microcystis Residence time (DSM2-PTM) (6.A.4.3) Results varied by subregion 28

Habitat Effects Microcystis Residence time (DSM2-PTM) (6.A.4.3) Potential for increases in south/central Delta, where Microcystis currently occurs (less abundant in north Delta – turbid conditions) Mitigate with preferential south Delta pumping 29

Tidal and Channel Margin Habitat Restoration Qualitative discussion; beneficial effects expected (potential for some adverse effects during construction) Localized Reduction of Predatory Fishes Measure intended for juvenile salmonids Georgiana Slough Nonphysical Fish Barrier Again, measure intended for juvenile salmonids 30

6.1.5 Effects of Monitoring Activities South Delta exports: salvage monitoring North Delta exports: impingement and entrainment (behind the screens) Other ongoing routine monitoring (not part of the PA, but would inform operations) 31

6.1.6 Cumulative Effects Qualitative discussion of: Water diversions Agricultural practices Increased urbanization Waste water treatment plants Other activities 32